Bioinformatics Sandbox | BioEdge India

DNA → Transcription → Translation

Paste a genomic or coding DNA sequence. The widget will strip FASTA headers, remove spaces, validate the bases, and translate into an amino acid chain with chemical-property highlighting.

Try Presets:

Live Sequence Analysis

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Sequence Length

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GC Content

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Melting Temp (T_m)

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Nucleotide Composition

Adenine (A)0 (0%)

Thymine (T) / Uracil (U)0 (0%)

Guanine (G)0 (0%)

Cytosine (C)0 (0%)

Output Sequences

Transcribed mRNA Sequence

Waiting for input...

Translated Protein Sequence (Chemical-Property Coded)

Waiting for input...

Hydrophobic/Nonpolar (A,V,L,I,P,F,W,M)

Polar/Uncharged (G,S,T,C,Y,N,Q)

Positively Charged/Basic (K,R,H)

Negatively Charged/Acidic (D,E)

Stop Codon (*)

Needleman-Wunsch Alignment

Global sequence alignment uses dynamic programming to construct an optimal scoring grid. Watch how gaps and mismatches shift the alignment path.

Sequence A

Sequence B

Match Score

Mismatch Penalty

Gap Penalty

Presets:

Alignment Result

Optimal alignment representation matching gap substitutions.

Run alignment to see results here.

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Alignment Score

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Sequence Identity

Interactive Dynamic Programming Matrix

The grid below displays calculated scores. Hover over any cell to review the three source scores (Diagonal, Up, Left) used to compute the maximum value. The optimal backtracking path is highlighted in glowing green.

📱Mobile Tip: Swipe left/right on the grid to scroll. For optimal mobile viewing, keep sequences under 15 characters.

Primer Designer & Reverse Translator

Convert functional amino acid targets (peptides) into optimized cDNA sequences and calculate high-efficiency Forward and Reverse PCR primers.

Input Peptide Chain (Single-Letter Codes)

Try Presets:

Host Expression Bias

Target Length: 20 bp

Primer Analysis Results

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Run the optimizer to design PCR primers and see details here.

Optimized cDNA Template

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Forward Primer (5' → 3')

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Length

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GC %

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T_m

Reverse Primer (5' → 3')

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Length

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GC %

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T_m

🧪 Virtual Agarose Gel Analysis (1.5% Gel)

Target: -

                Cathode (-)
              

                Anode (+)
              

Well 1 (Marker)

Well 2 (PCR)

Lane 1: 1kb Marker

Lane 2: PCR Amplicon

              • Ethidium Bromide (EtBr) simulation under 302nm UV light.
              • Smaller molecules encounter less frictional resistance and migrate faster towards the positive anode.
            

3D Molecular View

Use left-mouse click to rotate, right-mouse click to pan, and scroll-wheel to zoom in/out of the binding site.

Initializing WebGL environment...

Structure controls

Render high-resolution, three-dimensional structures right inside the browser using WebGL-cached models.

Select Molecule Preset

Display Representations

Cartoon/Ribbon Spacefill (Sphere) Sticks Lines

Interactive Interactions

Binding Pocket Analyzer

Dynamically isolate residues in close proximity to the ligand, calculate Euclidean distances, and screen for potential hydrogen bonds.

Interactive Bioinformatics Sandbox